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17 materials found

Keywords: Exploratory-analysis  or Flow cytometry data 


RNA-seq module Frederik Coppens

Material concerning RNA-seq analysis, with an emphasis on the statistical aspects.

Keywords: FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis

RNA-seq module Frederik Coppens https://tess.elixir-europe.org/materials/rna-seq-module-frederik-coppens-4a328fa8-0bef-471c-84e4-b0d89d216128 Material concerning RNA-seq analysis, with an emphasis on the statistical aspects. FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis
Flow Cytometry 2013 Module 4 - 1D Static gating

How to create a constant gate for the whole data set for one channel by first creating a sample representative of the whole data set How to apply a static gate to all samples and count the proportions of cells lying on either side of the gate Visualizing the proportions using a density...

Keywords: 1d static gating, Flow cytometry data

Flow Cytometry 2013 Module 4 - 1D Static gating https://tess.elixir-europe.org/materials/flow-cytometry-2013-module-4-1d-static-gating How to create a constant gate for the whole data set for one channel by first creating a sample representative of the whole data set How to apply a static gate to all samples and count the proportions of cells lying on either side of the gate Visualizing the proportions using a density plot, histogram, bean/violin plot Automating a sequential gating strategy in R to obtain cell proportions for a desired phenotype 1d static gating, Flow cytometry data 2013-06-26 2017-10-09
Flow Cytometry 2013 Module 6 - Clustering and Additional FCM Tools

Lecture on FlowCAP (Flow Cytometry: Critical Assessment of Population Identification Methods) project K-means explained flowMeans: smart k-means for FCM data flowClust3.0, SPADE, flowBin, flowFP, SamSPECTRAL clustering Biomarker discovery: flowType and RchyOptimyx, advanced tools used...

Keywords: Biomarker discovery, Flow cytometry data, Flowcap

Flow Cytometry 2013 Module 6 - Clustering and Additional FCM Tools https://tess.elixir-europe.org/materials/flow-cytometry-2013-module-6-clustering-and-additional-fcm-tools Lecture on FlowCAP (Flow Cytometry: Critical Assessment of Population Identification Methods) project K-means explained flowMeans: smart k-means for FCM data flowClust3.0, SPADE, flowBin, flowFP, SamSPECTRAL clustering Biomarker discovery: flowType and RchyOptimyx, advanced tools used to explore novel phenotypes and find ones which correlate with a clinical diagnosis More R: Bioconductor.org, an open source software project full of bioinformatics packages created for R, including sample work flows GenePattern.org: web-interface for running analysis modules such as sample deidentication, extracting specic keywords, quality control, normalization, clustering, classification FlowRepository.org: online FCM data repository to share public or private data sets with collaborators while providing detailed descriptions of the experiment set up and each FCS file Biomarker discovery, Flow cytometry data, Flowcap 2013-06-26 2017-10-09
Flow Cytometry 2013 Module 5 - 1D Dynamic gating

Using quantiles to set a gate based on a negative control Using median and standard deviation to set a gate based on a negative control Exploring rangeGate: an automated way to set a 1D gate for each sample individually Recording proportions of cells in subpopulations of interest by...

Keywords: 1d dynamic gating, Flow cytometry data

Flow Cytometry 2013 Module 5 - 1D Dynamic gating https://tess.elixir-europe.org/materials/flow-cytometry-2013-module-5-1d-dynamic-gating Using quantiles to set a gate based on a negative control Using median and standard deviation to set a gate based on a negative control Exploring rangeGate: an automated way to set a 1D gate for each sample individually Recording proportions of cells in subpopulations of interest by creating a spreadsheet file Recording a visual record of the gating results by creating JPEG image files 1d dynamic gating, Flow cytometry data 2013-06-26 2017-10-09
Flow Cytometry 2013 Module 3 - Preprocessing and Quality Assurance of FCM Data

Preprocessing Removing margin events Data transformation: log vs. biexponential Data normalization Quality Assurance Overview of quality assurance concepts: total raw/viable cell count, margin event count, outlier detection based on density of common...

Keywords: Flow cytometry data, Preprocessing, Quality assurance

Flow Cytometry 2013 Module 3 - Preprocessing and Quality Assurance of FCM Data https://tess.elixir-europe.org/materials/flow-cytometry-2013-module-3-preprocessing-and-quality-assurance-of-fcm-data Preprocessing Removing margin events Data transformation: log vs. biexponential Data normalization Quality Assurance Overview of quality assurance concepts: total raw/viable cell count, margin event count, outlier detection based on density of common parameters Building quality assurance objects using flowQ and generating summary HTML reports Flow cytometry data, Preprocessing, Quality assurance 2013-06-26 2017-10-09
Variant-calling

No description available

Keywords: Alignment, Annotation, BAM, BCF, De-novo-transcriptome-assembly, Exploratory-analysis, FASTQ, Pre-processing, QC, Statistical-model, Variant-calling, VCF

Variant-calling https://tess.elixir-europe.org/materials/variant-calling No description available Alignment, Annotation, BAM, BCF, De-novo-transcriptome-assembly, Exploratory-analysis, FASTQ, Pre-processing, QC, Statistical-model, Variant-calling, VCF
Day 4 - RNA-Seq Analysis

Day 4 focuses on the final steps after production of significant gene lists, including gene clustering, visualization, and annotation.

Keywords: Exploratory-analysis, Differential-expression, Statistical-model, Annotation

Day 4 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-4-rna-seq-analysis Day 4 focuses on the final steps after production of significant gene lists, including gene clustering, visualization, and annotation. Exploratory-analysis, Differential-expression, Statistical-model, Annotation
Statistics and RNA-Seq

This lecture and optional practical introduce the relevant statistical concepts along with its computational counterparts used on a common RNA-Seq data analysis workflow.

Keywords: FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis

Statistics and RNA-Seq https://tess.elixir-europe.org/materials/statistics-and-rna-seq This lecture and optional practical introduce the relevant statistical concepts along with its computational counterparts used on a common RNA-Seq data analysis workflow. FASTQ, Alignment, BAM, Differential-expression, Statistical-model, Exploratory-analysis
Material for the course RNA-seq data analysis with Chipster

This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis.

Scientific topics: RNA-Seq

Keywords: RNA-Seq, FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

Material for the course RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/material-for-the-course-rna-seq-data-analysis-with-chipster This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. RNA-Seq RNA-Seq, FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
Day 3 - RNA-Seq Analysis

Day 3 focuses on statistical analysis of RNA-Seq data and identification of differentiall expressed genes in multiple comparisons.

Keywords: QC, Exploratory-analysis, Differential-expression, Statistical-model, Pre-processing

Day 3 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-3-rna-seq-analysis Day 3 focuses on statistical analysis of RNA-Seq data and identification of differentiall expressed genes in multiple comparisons. QC, Exploratory-analysis, Differential-expression, Statistical-model, Pre-processing
RNA-Seq Analysis with Biocluster and R

Sequencing of RNA (RNA-Seq) is the latest method to assess global gene expression because it

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Alignment, Annotation, BAM, Differential-expression, Exploratory-analysis, Expression-estimation, FASTA, FASTQ, Feature-summarisation, Pre-processing, QC, Statistical-model

RNA-Seq Analysis with Biocluster and R https://tess.elixir-europe.org/materials/rna-seq-analysis-with-biocluster-and-r Sequencing of RNA (RNA-Seq) is the latest method to assess global gene expression because it RNA-Seq RNA-Seq, Alignment, Annotation, BAM, Differential-expression, Exploratory-analysis, Expression-estimation, FASTA, FASTQ, Feature-summarisation, Pre-processing, QC, Statistical-model
Material provided by Charlotte Soneson

This folder contains material provided by Charlotte Soneson. The following material is included:

Scientific topics: RNA-Seq

Keywords: RNA-Seq, Differential-expression, Statistical-model, Exploratory-analysis

Material provided by Charlotte Soneson https://tess.elixir-europe.org/materials/material-provided-by-charlotte-soneson This folder contains material provided by Charlotte Soneson. The following material is included: RNA-Seq RNA-Seq, Differential-expression, Statistical-model, Exploratory-analysis
RNA-seq module Eija Korpelainen

All material concerning RNA-seq data analysis with Chipster

Keywords: FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

RNA-seq module Eija Korpelainen https://tess.elixir-europe.org/materials/rna-seq-module-eija-korpelainen All material concerning RNA-seq data analysis with Chipster FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
Exercises for the course RNA-seq data analysis with Chipster

This practical covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis, using the free Chipster software. Material updated in Dec 2015.

Keywords: FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

Exercises for the course RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/exercises-for-the-course-rna-seq-data-analysis-with-chipster This practical covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis, using the free Chipster software. Material updated in Dec 2015. FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
Day 2 - RNA-Seq Analysis

Day 2 continues throught the steps in a typical RNA-Seq experiment from alignment to sample QC and count normalization, including a brief overview of the IGV Genome Browser.

Keywords: Alignment, BAM, FASTA, FASTQ, QC, Exploratory-analysis, Feature-summarisation, Pre-processing

Day 2 - RNA-Seq Analysis https://tess.elixir-europe.org/materials/day-2-rna-seq-analysis Day 2 continues throught the steps in a typical RNA-Seq experiment from alignment to sample QC and count normalization, including a brief overview of the IGV Genome Browser. Alignment, BAM, FASTA, FASTQ, QC, Exploratory-analysis, Feature-summarisation, Pre-processing
Lecture slides for the course RNA-seq data analysis with Chipster

This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. It discusses also experimental design. Material updated in Dec 2015.

Keywords: FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis

Lecture slides for the course RNA-seq data analysis with Chipster https://tess.elixir-europe.org/materials/lecture-slides-for-the-course-rna-seq-data-analysis-with-chipster This material covers the whole RNA-seq data analysis pipeline, from quality control of raw reads to differential expression analysis. It discusses also experimental design. Material updated in Dec 2015. FASTQ, QC, Pre-processing, Alignment, BAM, Expression-estimation, Feature-summarisation, Differential-expression, Statistical-model, Exploratory-analysis
Exploratory analysis and downstream analysis

This lecture gives an overview of exploratory analysis (clustering) and supervised analysis (prediction/classification), as well as visualization methods (heatmaps/PCA) and gene set analysis. It also shows how to transform count data to make it more suitable to apply the traditional methods...

Keywords: Statistical-model, Exploratory-analysis

Exploratory analysis and downstream analysis https://tess.elixir-europe.org/materials/exploratory-analysis-and-downstream-analysis This lecture gives an overview of exploratory analysis (clustering) and supervised analysis (prediction/classification), as well as visualization methods (heatmaps/PCA) and gene set analysis. It also shows how to transform count data to make it more suitable to apply the traditional methods developed (e.g.) for microarray data. Statistical-model, Exploratory-analysis